msmsTests

This is the development version of msmsTests; for the stable release version, see msmsTests.

LC-MS/MS Differential Expression Tests

Bioconductor version: Development (3.18)

Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

Author: Josep Gregori, Alex Sanchez, and Josep Villanueva

Maintainer: Josep Gregori i Font <josep.gregori at gmail.com>

Citation (from within R, enter citation("msmsTests")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("msmsTests")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("msmsTests")

msmsTests: controlling batch effects by blocking	PDF	R Script
msmsTests: post test filters to improve reproducibility	PDF	R Script
Reference Manual	PDF

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.39.0
In Bioconductor since	BioC 2.13 (R-3.0) (10 years)
License	GPL-2
Depends	R (>= 3.0.1), MSnbase, msmsEDA
Imports	edgeR, qvalue
Linking To
Suggests
System Requirements
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Depends On Me
Imports Me	MSnID
Suggests Me	RforProteomics
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	msmsTests_1.39.0.tar.gz
Windows Binary	msmsTests_1.39.0.zip (64-bit only)
macOS Binary (x86_64)	msmsTests_1.39.0.tgz
macOS Binary (arm64)	msmsTests_1.39.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msmsTests
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msmsTests
Bioc Package Browser	https://code.bioconductor.org/browse/msmsTests/
Package Short Url	https://bioconductor.org/packages/msmsTests/
Package Downloads Report	Download Stats